A class that holds Hbond objects and helps setup Hbonds for scoring. More...

#include <NPDHBondSet.hh>

Inheritance diagram for core::scoring::hbonds::NPDHBondSet:

Public Member Functions
	NPDHBondSet ()

	~NPDHBondSet () override

	NPDHBondSet (Size const nres)

	NPDHBondSet (HBondOptions const &options)

	NPDHBondSet (HBondOptions const &options, Size const nres)

	NPDHBondSet (pose::Pose &pose, EnergyMap const &weights)
	convenience constructor: Find all the hbonds in the pose. BB only default. More...

	NPDHBondSet (HBondOptions const &options, pose::Pose &pose, EnergyMap const &wights)
	convenience constructor: Find all the hbonds in the pose. BB only default. More...

	NPDHBondSet (NPDHBondSet const &src)
	copy ctor More...

	NPDHBondSet (NPDHBondSet const &src, utility::vector1< core::Size > const &exclude_list)
	NOTE: this is going to be wrong... More...

	NPDHBondSet (NPDHBondSet const &src, utility::vector1< bool > const &residue_mask)

	NPDHBondSet (NPDHBondSet const &src, Size seqpos)
	copy ctor More...

void	setup_for_residue_pair_energies (pose::Pose const &pose, bool const calculate_derivative=false)

basic::datacache::CacheableDataOP	clone () const override
	Clone this object. More...

void	show (std::ostream &out) const
	Print just the information stored in each individual hbond. More...

void	show () const

void	show (pose::Pose const &pose, bool const print_header, std::ostream &out) const
	Print nicely formated summary of the hbonds and their geometry in the pose. More...

void	show (pose::Pose const &pose, bool const print_header=true) const

void	show (pose::Pose const &pose, Size const residue, bool const print_header, std::ostream &out) const
	Print nicely formated summary of all the hbonds to a specific residue. More...

void	show (pose::Pose const &pose, Size const residue, bool const print_header=true) const

Real	hbond_weight (id::AtomID const &id, Size hbond_index) const
	Return the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom – stored in HBond::acc_index() or HBond::don_index()) More...

Real	d_hbond_weight_dE (id::AtomID const &id, Size hbond_fixed_index, Size hbond_changing_index) const
	Return the derivative of the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom ) as a function of the change in energy of another (possibly the same) hbond (by index) given the AtomID of the acceptor or the donor. More...

Real	dEtot_dEhb (Size hbond_index) const
	Return the derivative for the system induced by a change in energy of a particular hbond as caused by movement by its atoms. More...

Public Member Functions inherited from core::scoring::hbonds::HBondSet
	HBondSet ()

	~HBondSet () override

	HBondSet (Size const nres)

	HBondSet (HBondOptions const &options)

	HBondSet (HBondOptions const &options, Size const nres)

	HBondSet (pose::Pose &pose, bool const bb_only=true)
	Convenience constructor: Find all the hbonds in the pose. BB only default. More...

	HBondSet (HBondOptions const &options, pose::Pose &pose, bool const bb_only=true)
	Convenience constructor: Find all the hbonds in the pose. BB only default. More...

	HBondSet (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::scoring::hbonds::HBondDatabase const &database)
	Convenience constructor: Find all the hbonds between two residues. BB only default. More...

	HBondSet (HBondOptions const &options, core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::scoring::hbonds::HBondDatabase const &database)
	Convenience constructor: Find all the hbonds between two residues. BB only default. More...

	HBondSet (HBondSet const &src)
	copy ctor More...

	HBondSet (HBondSet const &src, utility::vector1< core::Size > exclude_list)
	copy ctor More...

	HBondSet (HBondSet const &src, utility::vector1< bool > residue_mask)
	copy ctor More...

	HBondSet (HBondSet const &src, Size seqpos)
	copy ctor More...

void	setup_for_residue_pair_energies (pose::Pose const &pose, bool const calculate_derivative=false, bool const backbone_only=true)

HBond const &	hbond (Size const number) const
	Access hbond. More...

HBondCOP	hbond_cop (Size const number) const
	Access hbond. More...

utility::vector1< HBondCOP >	atom_hbonds (AtomID const &atom, bool include_only_allowed=true) const
	Get a vector of the hbonds involving a particular atom. More...

utility::vector1< HBondCOP > const &	atom_hbonds_all (AtomID const &atom) const
	Get a reference to a vector of all the hbonds involving a particular atom; in contrast to "atom_hbonds" (above), this function does not exclude sc/bb hydrogen bonds. More...

utility::vector1< HBondCOP >	residue_hbonds (Size const seqpos, bool include_only_allowed=true) const
	Get a vector of all the hbonds involving this residue. More...

Size	nhbonds () const
	Number of hbonds. More...

utility::vector1< HBondOP > const &	hbonds () const
	Return the vector of HBond pointers. More...

Size	nhbonds (Size const seqpos, bool include_only_allowed=true) const
	Number of hbonds involving this residue. More...

Size	nhbonds (AtomID const &atom, bool include_only_allowed=true) const
	Number of hbonds involving this atom. More...

int	nbrs (Size const seqpos) const
	general function for accessing the number of 10A neighbors of a given position set by setup_for_residue_pair_energies. More...

HBondOptions const &	hbond_options () const
	Read access to the stored hbond options. More...

bool	allow_hbond (Size const index) const
	Is this hbond allowed under the bb-bb exclusion scheme? More...

bool	allow_hbond (HBond const &hbond) const

bool	acc_bbg_in_bb_bb_hbond (Size const residue) const
	is the backbone bone acceptor group in a bb/bb hydrogen bond? More...

bool	don_bbg_in_bb_bb_hbond (Size const residue) const
	is the backbone bone donor group in a bb/bb hydrogen bond? More...

void	append_hbond (Size const dhatm, conformation::Residue const &don_rsd, Size const aatm, conformation::Residue const &acc_rsd, HBEvalTuple const &hbe_tuple, Real const energy, Real const weight, HBondDerivs const &deriv)
	Add a new hbond to the list updates the "hbchk" array as necessary. More...

void	set_hbond_options (HBondOptions const &options)
	set the hbond options for this hbond set; clears all hbonds already stored More...

void	sort_by_weighted_energy ()

void	clear ()
	Delete all the data. More...

void	set_backbone_backbone_acceptor (Size const residue, bool state)
	Manually set the state of backbone-backbone acceptor. Used for symmetry. More...

void	set_backbone_backbone_donor (Size const residue, bool state)
	Manually set the state of backbone-backbone donor. Used for symmetry. More...

void	resize_bb_donor_acceptor_arrays (Size const new_dimension)
	Resize bb info arrays. More...

void	copy_bb_donor_acceptor_arrays (HBondSet const &src)

void	set_nbrs (Size const seqpos, Size value)
	Used by SymmetricScorFunction. Not sure why. Not for general use. More...

basic::datacache::CacheableDataOP	clone () const override
	Clone this object. More...

void	show (std::ostream &out) const
	Print just the information stored in each individual hbond. More...

void	show () const

void	show (pose::Pose const &pose, bool const print_header, std::ostream &out) const
	Print nicely formated summary of the hbonds and their geometry in the pose. More...

void	show (pose::Pose const &pose, bool const print_header=true) const

void	show (pose::Pose const &pose, Size const residue, bool const print_header, std::ostream &out) const
	Print nicely formated summary of all the hbonds to a specific residue. More...

void	show (pose::Pose const &pose, Size const residue, bool const print_header=true) const

Private Types
typedef id::AtomID	AtomID

typedef HBondSet	parent

Private Member Functions
void	derive_per_hbond_donor_and_acceptor_weights (pose::Pose const &pose)

void	get_weights_for_one_partner_hbonder (id::AtomID jj_id)

void	get_weights_for_two_partner_hbonder (id::AtomID jj_id)

void	sum_dEtot_dEhb_for_atom (id::AtomID const &jj_id)

Private Attributes
EnergyMap	sfxn_weights_
	The weights (in particular, for the npd_hbond_* terms) that will be used to determine the donor and acceptor weights. More...

id::AtomID_Map< utility::vector1< Real > >	atom_hbond_energies_
	One (unweighted) energy per hbond per atom. More...

id::AtomID_Map< utility::vector1< Real > >	atom_hbond_sfxn_wtd_energies_
	One score-function weighted energy per hbond per atom. More...

id::AtomID_Map< utility::vector1< Real > >	atom_hbond_weights_
	One weight per hbond per atom. More...

id::AtomID_Map< utility::vector1< utility::vector1< Real > > >	dwt_dE_for_hbond_
	d wt / d E so that this needs to be calculated only once per hydrogen bond More...

utility::vector1< Real >	dEtot_dEhb_

Friends
std::ostream &	operator<< (std::ostream &out, const NPDHBondSet &hbond_set)

bool	operator== (NPDHBondSet const &a, NPDHBondSet const &b)
	equality operator More...

Additional Inherited Members
Protected Member Functions inherited from core::scoring::hbonds::HBondSet
void	hbond_don_npd_weight (Size index, Real setting)
	allow the NPDHBondSet to store the npd weights in the hbond objects More...

void	hbond_acc_npd_weight (Size index, Real setting)
	allow the NPDHBondSet to store the npd weights in the hbond objects More...

Detailed Description

A class that holds Hbond objects and helps setup Hbonds for scoring.

For general hydrogen bond information, either use the default or option constructor, then use the fill methods in hbonds.hh OR use the convenience constructors to detect all Hbonds. Use the copy constructors to fill NPDHBondSets with the Hydrogen bonds you are interested in.

Member Typedef Documentation

◆ AtomID

typedef id::AtomID core::scoring::hbonds::NPDHBondSet::AtomID

private

◆ parent

typedef HBondSet core::scoring::hbonds::NPDHBondSet::parent

private

Constructor & Destructor Documentation

◆ NPDHBondSet() [1/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( )

◆ ~NPDHBondSet()

core::scoring::hbonds::NPDHBondSet::~NPDHBondSet ( )

overridedefault

◆ NPDHBondSet() [2/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( Size const nres )

◆ NPDHBondSet() [3/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( HBondOptions const & options )

◆ NPDHBondSet() [4/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet	(	HBondOptions const &	options,
		Size const	nres
	)

◆ NPDHBondSet() [5/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet	(	pose::Pose &	pose,
		EnergyMap const &	weights
	)

convenience constructor: Find all the hbonds in the pose. BB only default.

convenience constructor. If you need more controlled construction please use one of the other constructors

The pose must be non-const because the neighbor graph may need to be initialized.

References derive_per_hbond_donor_and_acceptor_weights().

◆ NPDHBondSet() [6/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet	(	HBondOptions const &	opts,
		pose::Pose &	pose,
		EnergyMap const &	weights
	)

convenience constructor: Find all the hbonds in the pose. BB only default.

convenience constructor. If you need more controlled construction please use one of the other constructors

The pose must be non-const because the neighbor graph may need to be initialized.

References derive_per_hbond_donor_and_acceptor_weights().

◆ NPDHBondSet() [7/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet ( NPDHBondSet const & src )

copy ctor

◆ NPDHBondSet() [8/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet	(	NPDHBondSet const &	src,
		utility::vector1< core::Size > const &	exclude_list
	)

NOTE: this is going to be wrong...

◆ NPDHBondSet() [9/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet	(	NPDHBondSet const &	src,
		utility::vector1< bool > const &	residue_mask
	)

◆ NPDHBondSet() [10/10]

core::scoring::hbonds::NPDHBondSet::NPDHBondSet	(	NPDHBondSet const &	src,
		Size	seqpos
	)

copy ctor

Member Function Documentation

◆ clone()

basic::datacache::CacheableDataOP core::scoring::hbonds::NPDHBondSet::clone ( ) const

override

Clone this object.

clone this object

◆ d_hbond_weight_dE()

Real core::scoring::hbonds::NPDHBondSet::d_hbond_weight_dE	(	id::AtomID const &	id,
		Size	hbond_fixed_index,
		Size	hbond_changing_index
	)		const

Return the derivative of the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom ) as a function of the change in energy of another (possibly the same) hbond (by index) given the AtomID of the acceptor or the donor.

References dwt_dE_for_hbond_.

◆ derive_per_hbond_donor_and_acceptor_weights()

void core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights ( pose::Pose const & pose )

private

Referenced by NPDHBondSet(), and setup_for_residue_pair_energies().

◆ dEtot_dEhb()

Real core::scoring::hbonds::NPDHBondSet::dEtot_dEhb ( Size hbond_index ) const

Return the derivative for the system induced by a change in energy of a particular hbond as caused by movement by its atoms.

References dEtot_dEhb_.

◆ get_weights_for_one_partner_hbonder()

void core::scoring::hbonds::NPDHBondSet::get_weights_for_one_partner_hbonder ( id::AtomID jj_id )

private

References atom_hbond_energies_, atom_hbond_sfxn_wtd_energies_, atom_hbond_weights_, core::scoring::hbonds::HBondSet::atom_hbonds_all(), dwt_dE_for_hbond_, core::scoring::hbonds::get_weights_for_one_partner_hbonder(), core::scoring::hbonds::HBondSet::hbond(), and core::id::AtomID_Map< T >::resize().

Referenced by derive_per_hbond_donor_and_acceptor_weights().

◆ get_weights_for_two_partner_hbonder()

void core::scoring::hbonds::NPDHBondSet::get_weights_for_two_partner_hbonder ( id::AtomID jj_id )

private

References atom_hbond_energies_, atom_hbond_sfxn_wtd_energies_, atom_hbond_weights_, core::scoring::hbonds::HBondSet::atom_hbonds_all(), dwt_dE_for_hbond_, core::scoring::hbonds::get_weights_for_two_partner_hbonder(), core::scoring::hbonds::HBondSet::hbond(), and core::id::AtomID_Map< T >::resize().

Referenced by derive_per_hbond_donor_and_acceptor_weights().

◆ hbond_weight()

Real core::scoring::hbonds::NPDHBondSet::hbond_weight	(	id::AtomID const &	id,
		Size	hbond_index
	)		const

Return the non-pairwise-decomposable weight for a particular atom for a particular hbond (by index for that atom – stored in HBond::acc_index() or HBond::don_index())

References atom_hbond_weights_.

◆ setup_for_residue_pair_energies()

void core::scoring::hbonds::NPDHBondSet::setup_for_residue_pair_energies	(	pose::Pose const &	pose,
		bool const	calculate_derivative = `false`
	)

References derive_per_hbond_donor_and_acceptor_weights(), and core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies().

◆ show() [1/6]

void core::scoring::hbonds::NPDHBondSet::show ( ) const

References core::scoring::hbonds::TR().

Referenced by show().

◆ show() [2/6]

void core::scoring::hbonds::NPDHBondSet::show	(	pose::Pose const &	pose,
		bool const	print_header,
		std::ostream &	out
	)		const

Print nicely formated summary of the hbonds and their geometry in the pose.

@detail Optionally print a header, and then a row for each hydrogen bond in the set using the iterprable version of the hbond show format formatted for easy parsing by R, Excel, etc.

References core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), core::conformation::membrane::out, and core::scoring::hbonds::HBond::show().

◆ show() [3/6]

void core::scoring::hbonds::NPDHBondSet::show	(	pose::Pose const &	pose,
		bool const	print_header = `true`
	)		const

References show(), and core::scoring::hbonds::TR().

◆ show() [4/6]

void core::scoring::hbonds::NPDHBondSet::show	(	pose::Pose const &	pose,
		Size const	residue_number,
		bool const	print_header,
		std::ostream &	out
	)		const

Print nicely formated summary of all the hbonds to a specific residue.

@detail Optionally print a header, and then a row for each hydrogen bond in the set using the iterprable version of the hbond show format formatted for easy parsing by R, Excel, etc.

References core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), core::conformation::membrane::out, and core::scoring::hbonds::HBond::show().

◆ show() [5/6]

void core::scoring::hbonds::NPDHBondSet::show	(	pose::Pose const &	pose,
		Size const	residue,
		bool const	print_header = `true`
	)		const

References show(), and core::scoring::hbonds::TR().

◆ show() [6/6]

void core::scoring::hbonds::NPDHBondSet::show ( std::ostream & out ) const

Print just the information stored in each individual hbond.

References core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), and core::conformation::membrane::out.

◆ sum_dEtot_dEhb_for_atom()

void core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom ( id::AtomID const & jj_id )

private

References core::scoring::hbonds::HBond::acc_npd_weight(), core::scoring::hbonds::HBondSet::atom_hbonds_all(), dEtot_dEhb_, core::scoring::hbonds::HBond::don_npd_weight(), dwt_dE_for_hbond_, core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::HBond::index(), core::scoring::hbonds::HBondSet::nhbonds(), and core::id::AtomID::rsd().

Referenced by derive_per_hbond_donor_and_acceptor_weights().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		const NPDHBondSet &	hbond_set
	)

friend

◆ operator==

bool operator==	(	NPDHBondSet const &	a,
		NPDHBondSet const &	b
	)

friend

equality operator

Member Data Documentation

◆ atom_hbond_energies_

id::AtomID_Map< utility::vector1< Real > > core::scoring::hbonds::NPDHBondSet::atom_hbond_energies_

private

One (unweighted) energy per hbond per atom.

Referenced by derive_per_hbond_donor_and_acceptor_weights(), get_weights_for_one_partner_hbonder(), and get_weights_for_two_partner_hbonder().

◆ atom_hbond_sfxn_wtd_energies_

id::AtomID_Map< utility::vector1< Real > > core::scoring::hbonds::NPDHBondSet::atom_hbond_sfxn_wtd_energies_

private

One score-function weighted energy per hbond per atom.

Referenced by derive_per_hbond_donor_and_acceptor_weights(), get_weights_for_one_partner_hbonder(), and get_weights_for_two_partner_hbonder().

◆ atom_hbond_weights_

id::AtomID_Map< utility::vector1< Real > > core::scoring::hbonds::NPDHBondSet::atom_hbond_weights_

private

One weight per hbond per atom.

Referenced by derive_per_hbond_donor_and_acceptor_weights(), get_weights_for_one_partner_hbonder(), get_weights_for_two_partner_hbonder(), and hbond_weight().

◆ dEtot_dEhb_

utility::vector1< Real > core::scoring::hbonds::NPDHBondSet::dEtot_dEhb_

private

Referenced by derive_per_hbond_donor_and_acceptor_weights(), dEtot_dEhb(), and sum_dEtot_dEhb_for_atom().

◆ dwt_dE_for_hbond_

id::AtomID_Map< utility::vector1< utility::vector1< Real > > > core::scoring::hbonds::NPDHBondSet::dwt_dE_for_hbond_

private

d wt / d E so that this needs to be calculated only once per hydrogen bond

Referenced by d_hbond_weight_dE(), derive_per_hbond_donor_and_acceptor_weights(), get_weights_for_one_partner_hbonder(), get_weights_for_two_partner_hbonder(), and sum_dEtot_dEhb_for_atom().

◆ sfxn_weights_

EnergyMap core::scoring::hbonds::NPDHBondSet::sfxn_weights_

private

The weights (in particular, for the npd_hbond_* terms) that will be used to determine the donor and acceptor weights.

The documentation for this class was generated from the following files:

src/core/scoring/hbonds/NPDHBondSet.hh
src/core/scoring/hbonds/NPDHBondSet.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AtomID

◆ parent

Constructor & Destructor Documentation

◆ NPDHBondSet() [1/10]

◆ ~NPDHBondSet()

◆ NPDHBondSet() [2/10]

◆ NPDHBondSet() [3/10]

◆ NPDHBondSet() [4/10]

◆ NPDHBondSet() [5/10]

◆ NPDHBondSet() [6/10]

◆ NPDHBondSet() [7/10]

◆ NPDHBondSet() [8/10]

◆ NPDHBondSet() [9/10]

◆ NPDHBondSet() [10/10]

Member Function Documentation

◆ clone()

◆ d_hbond_weight_dE()

◆ derive_per_hbond_donor_and_acceptor_weights()

◆ dEtot_dEhb()

◆ get_weights_for_one_partner_hbonder()

◆ get_weights_for_two_partner_hbonder()

◆ hbond_weight()

◆ setup_for_residue_pair_energies()

◆ show() [1/6]

◆ show() [2/6]

◆ show() [3/6]

◆ show() [4/6]

◆ show() [5/6]

◆ show() [6/6]

◆ sum_dEtot_dEhb_for_atom()

Friends And Related Function Documentation

◆ operator<<

◆ operator==

Member Data Documentation

◆ atom_hbond_energies_

◆ atom_hbond_sfxn_wtd_energies_

◆ atom_hbond_weights_

◆ dEtot_dEhb_

◆ dwt_dE_for_hbond_

◆ sfxn_weights_